International Journal of Molecular Sciences Review Evolution of Influenza A Virus by Mutation and Re-Assortment Wenhan Shao 1, Xinxin Li 1, Mohsan Ullah Goraya 1, Song Wang 1,* and Ji-Long Chen 1,2,* 1 Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; [email protected] (W.S.); [email protected] (X.L.); [email protected] (M.U.G.) 2 CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China * Correspondence: [email protected] (S.W.); [email protected] (J.-L.C.); Tel.: +86-591-8375-8852 (S.W.); +86-591-8378-9159 (J.-L.C.) Received: 25 June 2017; Accepted: 24 July 2017; Published: 7 August 2017 Abstract: Influenza A virus (IAV), a highly infectious respiratory pathogen, has continued to be a significant threat to global public health. To complete their life cycle, influenza viruses have evolved multiple strategies to interact with a host. A large number of studies have revealed that the evolution of influenza A virus is mainly mediated through the mutation of the virus itself and the re-assortment of viral genomes derived from various strains. The evolution of influenza A virus through these mechanisms causes worldwide annual epidemics and occasional pandemics. Importantly, influenza A virus can evolve from an animal infected pathogen to a human infected pathogen. The highly pathogenic influenza virus has resulted in stupendous economic losses due to its morbidity and mortality both in human and animals. Influenza viruses fall into a category of viruses that can cause zoonotic infection with stable adaptation to human, leading to sustained horizontal transmission. The rapid mutations of influenza A virus result in the loss of vaccine optimal efficacy, and challenge the complete eradication of the virus. In this review, we highlight the current understanding of influenza A virus evolution caused by the mutation and re-assortment of viral genomes. In addition, we discuss the specific mechanisms by which the virus evolves. Keywords: influenza A virus; mutation; re-assortment; virus-host interaction 1. Introduction In both the northern and southern parts of the world, the outbreaks of influenza occur mainly in winter, while in areas around the equator outbreaks may occur at any time of the year. Typically, influenza is transmitted from infected mammals through the air by cough or sneezing, and also from infected birds through their droppings. Influenza virus can also be transmitted through saliva, nasal secretions, feces, and blood of the infected animals. In humans, the common symptoms of influenza virus infection are fever, muscle pain, severe headache, coughing, sore throat, weakness, and fatigue. Influenza virus, which belongs to the family of Orthomyxoviridae, consists of eight segments of negative-sense single-stranded RNA. The orthomyxoviridae is further divided into five genera: influenza A virus (IAV), influenza B virus, influenza C virus, isavirus, and thogotovirus [1]. Influenza B and C viruses only infect humans, causing the respiratory disease [2,3]. IAV poses a significant risk of zoonotic infection, host switch, and the generation of pandemic viruses. IAVs can infect humans and a variety of animals, such as pigs, horses, marine mammals, cats, dogs, and birds. Although the history of IAV seems to originate from ancient Greek in about 413 BC [4], the first confirmed pandemic was the Russian flu that occurred in 1889–1892 [5]. Int. J. Mol. Sci. 2017, 18, 1650; doi:10.3390/ijms18081650 www.mdpi.com/journal/ijms Int. J. Mol. Sci. 2017, 18, 1650 2 of 13 There are three main characteristics which contribute to the rapid evolution of these viruses: large populations, short generation times, and high mutation rates. Every mutation, which helps the virus to evade the host immune system, may be positively selected, passed on to the next generation, and distributed more widely. Over the past 100 years, there have been four flu pandemics: 1918 H1N1 Spanish flu [6], which has been described as “the greatest medical holocaust in history” [7], 1957 H2N2 Asian flu, 1968 H3N2 Hong Kong flu, and 2009 H1N1 swine flu. The most serious pandemic occurred in 1918, killing more than 50 million people worldwide [8]. Since 1996, the highly pathogenic avian influenza (HPAI) virus (H5N1) has caused more than 1000 deaths, resulting in a mortality rate of about 55% [9]. Recently, a low-pathogenic avian influenza (LPAI) virus (H7N9) identified first in the East China region caused an outbreak in humans, with a mortality rate as high as 40% [10]. 2. Classification of the Virus The influenza virus genome is about 13kb and encodes 13 proteins [11]: Hemagglutinin (HA), neuraminidase (NA), M1 matrix protein (M1), M2 ion channel protein (M2), nuclear protein (NP), nonstructural protein (NS1, NS2), and RNA polymerase complex (PB1, PB2, PA) [12]. On the basis of their surface glycoproteins, HA and NA, influenza A viruses can be divided into 18 HA subtypes and 11 NA subtypes, and further classified by strains, while influenza B and C viruses are classified only by strains [3,13]. The IAV genes encoding the viral surface proteins, HA and NA, that form the main targets of neutralizing antibodies, are critical for the evolution of the virus. HA is a trimeric glycoprotein, and each monomer has two polypeptide chains: HA1 and HA2. There are 16 classical subtypes of HA which are classified in two groups and four clades: group 1 contains the H1 clade (H1, H2, H5, H6, H11, H13, H16) and the H9 clade (H8, H9, H12), while group 2 includes the H3 clade (H3, H4, H14) and the H7 clade (H7, H10, H15) [14,15]. Recently, two more HA subtypes have been discovered exclusively in bats (H17 and H18) [16]. NA is a tetramer of four identical polypeptide chains. The nine classical subtypes of NA are divided into three groups: Group 1 comprises N1, N4, N5, N8, group 2 comprises N2, N3, N6, N7, N9, and group 3 contains NA of influenza B viruses. Recently, two new NA subtypes have been found in bats (N10 and N11) [16]. Human influenza viruses have only limited subtypes of HA and NA, including H1, H2, H3 and N1, N2, whereas influenza viruses that infect poultry may include almost all subtypes of HA and NA [17]. 3. IAV Life Cycle and Host Antiviral Response IAV membrane protein HA plays an important role in the establishment of viral infection. The influenza virus binds to the sialic acid on the cellular glycoprotein or glycolipid through the outer side of the head of the HA molecule. Specific sialic acid linkages and penultimate galactose determine the host specificity of the virus. For example, the HA of human adapted influenza virus preferentially recognizes receptors with a terminal α-2,6 sialic acid (SA), whereas the avian IAV preferentially recognizes receptors with a terminal α-2,3 SA [11,18]. The α-2,6 SA are found on bronchial epithelial cells of the human upper respiratory tract (URT) and the α-2,3 SA are found on epithelial cells of the birds’ intestine and on the lower respiratory tract (LRT) of humans [15]. Thus, differences of cell surface receptors constitute a major barrier to cross-species transmission of influenza virus. HA is a HA1-HA2 dimer linked by disulfide bonds formed by the hydrolysis of HA0 precursor [19]. HA1 has a functional domain that binds to the host cell receptor, and HA2 is an important subunit that mediates the fusion of the virus with the host cell membrane. Therefore, influenza virus enters the host cell through HA1-mediated binding with the cell receptor, followed by HA2-mediated virus fusion with the cellular membrane and finally the invasion of host cells [20]. The cleavage of the IAV particles from the binding site of the host cell surface is mediated by the action of the viral NA [19]. NA has an enzymatic activity to promote the dispersion of influenza virus in respiratory mucosal secretions [21]. It is important that NA enzymatic activity removes sialic acid from viruses and cellular glycoproteins to facilitate the release of progeny virus particles from cells Int. J. Mol. Sci. 2017, 18, 1650 3 of 13 and then infect the other cells [22–24]. Because HA and NA are responsible for the binding to and the release from host cell receptors, they are crucial in determining host specificity [25]. The virulence of IAVs is largely dependent on the coordination of HA and NA. It has been observed that the HA/NA balance is one of the key factors in the transmission of NA inhibitor-resistant strains in the human population [26]. Unlike many other RNA viruses, the replication and transcription of influenza viruses are carried out in the nucleus of the host cell. Within the influenza virus particles, the NP binds to the viral RNA gene segment and the viral RNA polymerase complex binds to the end of the viral RNA, and they together form the vRNP containing the RNA-protein complex [27]. Influenza virus vRNP is the basic replication unit of influenza virus, composed by the virus RNA and four kinds of viral proteins including NP, PB1, PB2, and PA [28,29]. PB1, PB2, and PA together constitute an RNA polymerase complex that is critically involved in the genomic replication and expression of influenza virus [29]. In addition, the pathogenicity of IAV is associated with the host immunity [30,31]. IAV infection induces host innate immune responses, which can result in the termination of the virus life cycle. On the other hand, influenza virus has evolved multiple strategies to circumvent the host’s innate immunity to establish a successful infection and replication [32,33].